title: h1_RNA_leaves_rep3

first: Jaemyung

last: Choi

address: Norwich Research Park

institute: John Innes Centre

description:
h1_leaf.f.bw
h1_leaf.r.bw

data_processing:
Illumina Hiseq basecalls were performed using 'bcl2fq' at the U.C.Berkeley sequencing core facility.
For bisulfite-seq, reads were mapped with bowtie and bs-sequel pipeline (https://zilbermanlab.net/tools/) allowing up to 2 mismatches.
For RNA-seq libraries, reads were mapped with HISAT2 with following options: --max-intronlen 10000 -k 2 --dta. we kept uniquely mapped reads for annotating TE genes and antisense transcripts with StringTie.
For decap-seq libraries, adapter sequences were trimmed using CUTADAPT, leaving reads longer than 20 bp. Adapter-trimmed reads were mapped with HISAT2 with following options: --max-intronlen 10000 -k 2 --dta.
For ChIP- and ChAP-seq, reads were mapped with Bowtie allowing up to 2 mismatches and normalized by RPKM. Log 2 ratio between IP- or AP-ed and input was calculated by bamcompare function in deepTools2.
For DNase-seq read were mapped with Bowtie and normalized by RPKM with a Perl script 'window_alignment' and 'gff_arithmetics' (https://zilbermanlab.net/tools/).
Genome_build: TAIR10
Supplementary_files_format_and_content: For bisulfite-seq, GFF files contain DNA methylation of average 50 bp windows. For other data, bigwig files contain log2 ratio between treated and input sampes

source_name: leaf tissue

extract_protocol: 1 mg of RNA was subjected to DNA-free DNA removal kit (Thermo, AM1907) to degrade DNA from samples. To remove rRNA, RNA was treated with Ribo-zero plant kit (Illumina, MRZPL1224).

value: leaf tissue


title: uninjured_1

status: Public on Nov 20 2019

type: SRA

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

library_source: transcriptomic

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 (GRCz11) using STAR 2.6.0c with the parameter “--outFilterMismatchNoverLmax 0.1 --alignIntronMax 200000” (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 12.04.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: danrer11 / GRCz11
Supplementary_files_format_and_content: The tab-delimited matrix with DESeq normalized counts.

molecule: polyA RNA

organism: Danio rerio

source_name: 2 hearts

extract_protocol:
For RNA-seq, RNA was isolated from the laser microdissected samples using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip GxTouch 24 (Perkin Elmer).
20 ng of total RNA was used as input for PolyA enrichment (NEXTflexTM PolyA Beads) followed by library preparation using NEXTflexTM Rapid Directional qRNA-SeqTM Kit (Bioo Scientific Corp). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in average of 38M reads per library with 2x75bp paired end setup.

treatment_protocol: Valve cell ablation was performed by treating the fish with 2.5 mM Metronidazole for 6 hours. Fish were treated in individual containers and were kept in the dark during treatments.

tag: time after injury

value: uninjured


title: IEL1817_3

city: Freiburg

first: Patrice

last: Zeis

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
For image aquisition, intensity extraction and basecalling HiSeq Control Software  2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000) was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. This procedure resulted in 34,111 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the unique molecular identifier (UMI) followed by six bases representing the cell specific barcode. The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9
Supplementary_files_format_and_content: CSV files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

molecule: total RNA

organism: Mus musculus

source_name: library of 96 TBGR C-mycfl/fl  IELP cells

growth_protocol: Mice were housed under SPF condition at the department of medical microbiology and hygiene of the university medical center Freiburg in accordance with the local animal care committiees and Regierungspräsidium Freiburg

extract_protocol:
IELPs were isolated by dissecting the thymus and single cell suspension of the thymus was isolated by mashing the tissue through a 70µm cell strainer with 15ml PBS. Lymphocytes were enriched by performing red cell lysis and IELPs were enriched by depleting CD4+ and CD8+ thymocytes by incubation with anti-CD4 and anti-CD8 purified antibodies and anti-mouse Dynabeads.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol

tag: strain background

value: TBGR

tag: genotype/variation

value: C-mycfl/fl

tag: age

value: 2 wk

tag: tissue

value: Thymus

tag: cell type

value: intraepithelial lymphocytes (IELs)


title: poly(A)-depletion, jird, 20 dpi immature male, a, SRX1539752

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

country: USA

institute: University of Maryland School of Medicine

description:
wbm_counts.txt
wbm_tpm.txt

data_processing:
Reads aligned to a combined A. aegypti, B. malayi, and wBm reference using TopHat v1.4 (for poly(A) selection and B. malayi Agilent SureSelect samples) or Bowtie v0.12.9 (for poly(A) depletion and wBm Agilent SureSelect samples)
Protein-coding genes for B. malayi and A. aegypti quantified using HTSeq v0.5.3p9 with mode set to union. Protein-coding genes for wBm quantified using FADU v1.2.
Differentially expressed genes for all three organisms were individually identified using edgeR v3.20.1
TPM values calculated for protein-coding genes
Expression modules for differentially expressed genes for all three organisms identified using WGCNA v1.61
Significantly over-represented functional terms identified using Fisher's exact test for each WGCNA module
Genome_build: Brugia malayi WS259, Wolbachia endosymbiont strain TRS of Brugia malayi (NC_006833.1), and Aedes aegypti AaegL3.3
Supplementary_files_format_and_content: tab-delimited files containing counts, TPM, WGCNA module assignments for differentially expressed genes, functional term enrichment analyses for WGCNA modules for both B. malayi and A. aegypti

organism:
Brugia malayi
Wolbachia endosymbiont of Brugia malayi

source_name: B. malayi immature males taken from jirds 20 dpi

extract_protocol:
For nematode samples, third stage larvae of Brugia malayi strain FR3 were isolated from infected mosquitoes 9-16 days post infection (dpi) using the NIAID/NIH Filariasis Research Reagent Resource Center (FR3) Research Protocol 8.4. Larvae were isolated in RPMI + P/S, enumerated, and either flash frozen in liquid nitrogen for storage at -80°C or used for the infection of male Mongolian gerbils (Meriones unguiculatus; Charles River, Wilmington, MA, USA). Gerbils were anesthetized with 5% isoflurane and infected by introducing 400 L3s into the peritoneal cavity using a butterfly catheter. Larvae, immature adults, and mature adults were recovered by peritoneal flush using a terminal procedure. Brugia malayi embryos were collected from live gravid females as previously described. For vector samples, the Aedes aegypti black-eyed Liverpool strain was obtained from FR3 and maintained in the Biosafety Level 2 Insectary at the University of Wisconsin Oshkosh. Desiccated mosquito eggs were hatched in deoxygenated water and the resulting larvae were maintained on a slurry of ground TetraMin fish food (Blacksburg, VA) at 27°C with 80% relative humidity. Female pupae were separated using a commercial larva pupa separator (The John Hock Company, Gainesville, FL), placed in mesh-covered paper soup cartons, and enclosed adults were fed with cotton pads soaked in sucrose solution. Females were deprived of sucrose approximately twelve hours prior to blood feeding. Mosquitoes were infected with the Brugia malayi FR3 strain by feeding microfilaremic cat blood (FR3) through Parafilm via a glass-jacketed artificial membrane feeder. When necessary microfilaremic cat blood was diluted with uninfected dog blood to achieve a suitable parasite density for infection (100-250 microfilariae/20 μL). Infected mosquitoes were collected at 18 hours post infection (hpi), 4 dpi, and 8 dpi. They were anesthetized with CO2 then transferred to chilled microscope slides where the legs, wings, heads and abdomens were removed. The thoraces with and without developing B. malayi larvae were flash frozen in liquid nitrogen and stored at -80 °C prior to RNA isolation. Vector-derived Infective B. malayi L3 were isolated from whole mosquitoes in bulk using the standard FR3 protocol. For RNA isolation, mosquito thoraces were combined with TRIzol (Zymo Research, Irvine, CA) at a ratio of 1 mL TRIzol per 50-100 mg mosquito tissue, while nematode samples were processed using a 3:1 volume ratio of TRIzol to sample. For both preparations, 1 µL β-mercaptoethanol was added for every 100 µL of sample. The tissues were homogenized using a bead beater and a TissueLyser (Qiagen, Germantown, MD) at 50 Hz for 5 min. The homogenate was then transferred to a new tube and centrifuged at 12,000g for 10 min at 4°C. After incubation at room temperature for 5 min, 0.2 mL chloroform was added for every 1 mL TRIzol. The samples were shaken by hand for 15 s, incubated at room temperature for 3 min, loaded into a pre-spun Phase Lock Gel heavy tube (5Prime, Gaithersburg, MD), and centrifuged at 12,000g for 5 min at 4°C. The upper phase was extracted, one volume of 100% ethanol was added, and then loaded onto a PureLink RNA Mini column (Ambion, Austin, TX). The samples were processed following manufacturer instructions, quantified using a Qubit fluorometer (Qiagen, Germantown, MD) and Nanodrop spectrometer (Nanodrop, Wilmington, DE), and sent to Institute for Genomic Sciences at the University of Maryland Baltimore for DNase treatment and library preparation.
Whole transcriptome libraries without AgSS capture were constructed for sequencing on the Illumina platform using the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA). For targeting eukaryotic mRNA, polyadenylated RNA was isolated using the NEBNext Poly(A) mRNA magnetic isolation module. For the B. malayi and wBm AgSS capture designs, probes were designed using the SureSelect DNA Advanced Design Wizard for B. malayi and wBm. When targeting bacterial mRNA, samples underwent rRNA- and poly(A)-reductions. Probes were designed to capture every 120 bp for each coding sequence in both organisms with no overlap between baits. DustMasker was used to identify and mask low complexity regions of the genome from the probe design .For samples treated with the wBm AgSS capture, pre-capture libraries were constructed from 500-1000 ng of total RNA samples using the NEBNext Ultra Directional RNA Library Prep kit (NEB, Ipswich, MA, USA). First strand cDNA was synthesized without mRNA extraction to retain non-polyadenylated transcripts and fragmented at 94 oC for 8 min. After adaptor ligation, cDNA fragments were amplified with 10 cycles of PCR before capture. Wolbachia transcripts were captured from 200 ng of the amplified libraries using the Agilent SureSelectXT RNA (0.5-2 Mbp) bait library designed specifically for wBm. Library-bait hybridization reactions were incubated at 65 °C for 24 h then bound to MyOne Streptavidin T1 dynabeads (Invitrogen, Carlsbad, CA, USA). After multiple washes, bead-bound captured library fragments were amplified with 18 cycles of PCR. The libraries were loaded on an Illumina HiSeq4000, generating 151-bp paired end reads. For samples treated with the B. malayi AgSS capture, pre-capture libraries were constructed from 1000 ng of total RNA samples using the NEBNext Ultra Directional RNA Library Prep kit (NEB #E7420, Ipswich, MA, USA). After adaptor ligation, cDNA fragments were amplified for 10 cycles of PCR before capture. B. malayi transcripts were captured from 200 ng of the amplified libraries using an Agilent SureSelectXT Custom (12-24 Mbp) bait library designed specifically for B. malayi. Library-bait hybridization reactions were incubated at 65 °C for 24 h then bound to MyOne Streptavidin T1 Dynabeads (Invitrogen, Carlsbad, CA). After multiple rounds of washes, bead-bound captured library fragments were amplified with 16 cycles of PCR. The libraries were loaded on a Illumina HiSeq 4000 generating 151-bp paired end reads.

tag: brugia malayi strain

tag: enrichment method

value: rRNA-, poly(A)-depletion


title: IEL1817_4


title: h1_RNA_leaves_rep2

city: Norwich

department: Cell and Developmental Biology

country: United Kingdom

description:
h1_leaf.f.bw
h1_leaf.r.bw

organism: Arabidopsis thaliana

growth_protocol: Around 200 seeds were germinated and grown in half strength Gamborg's B5 media for 2-4 weeks under continuous light. h1.1 h1.2 plants (Zemach et al., 2013) were crossed to met1-6 +/- (Xiao et al., 2003) to genenrate h1.1 h1.2 met1-6 triple knockout mutants. After crossing, h1.1 h1.2 met1-6 +/- were isolated at F2 generation, then homozygous triple knockout mutants were indentified at F3. F4 homozygous mutant plants were used for sequencing.


title: 48hpab_1

value: 48 hours


title: IEL1817_2


title: h1_RNA_leaves_rep1

description:
h1_leaf.f.bw
h1_leaf.r.bw
col_leaf.r.bw


title: poly(A)-selection, jird, embryo, b, SRX1539751

description:
bmalayi_counts.txt
bmalayi_tpm.txt

source_name: B. malayi embryos taken from jirds

tag: developmental stage

value: jird, embryo

value: poly(A)-enrichment


title: IEL1817_1


title: poly(A)-depletion, jird, 8 dpi, b, SRX1539750

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi taken from jirds 8 dpi


title: IELKO15_1

source_name: library of 96 TBGR C-mycD/DCd4 IELP cells


title: IEL1516_4


title: poly(A)-depletion, jird, 8 dpi, a, SRX1539748

description:
wbm_counts.txt
wbm_tpm.txt


title: h1met1_RNA_rep2

description:
processed_data_file: h1met1_seedling.f.bw
processed_data_file: h1met1_seedling.r.bw

source_name: 2 week old seedlings

value: 2 week old seedlings


title: h1met1_RNA_rep1


title: poly(A)-selection, jird, embryo, a, SRX1539746

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: IEL1516_3


title: poly(A)-depletion, jird, 4 dpi, b, SRX1539745

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi taken from jirds 4 dpi


title: met1_RNA_rep3

description:
processed_data_file: met1_seedling.f.bw
processed_data_file: met1_seedling.r.bw


title: IEL1516_1


title: poly(A)-depletion, jird, 3 dpi, b, SRX1539742

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi taken from jirds 3 dpi


title: wBm Agilent SureSelect, jird, 24 dpi immature female, a, SRX2508257

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi immature females taken from jirds 24 dpi

value: wBm Agilent SureSelect capture


title: met1_RNA_rep2


title: wBm Agilent SureSelect, jird, adult female, c, SRX2508256

description:
wbm_counts.txt
wbm_tpm.txt

source_name: B. malayi adult females taken from jirds


title: poly(A)-depletion, jird, 3 dpi, a, SRX1539741

description:
wbm_counts.txt
wbm_tpm.txt


title: Rhabdo - anti-miR-22 7

type: RNA

city: Berlin

first: Michael

last: Fähling

address: Charitéplatz 1

department: Institut für Vegetative Physiologie

institute: Charité - Universitätsmedizin Berlin

description: AKI animals & miR-22 inhibitor

hyb_protocol: The hybridization in the Affymetrix hybridization oven 640 at 45°C and 60 rpm for 16 h, the staining and washing, processed in the Fluidics Station 450.

scan_protocol: GeneChipScanner 3000 G7 system (as recommended by Affymetrix (Affymetrix Inc., Santa Clara, CA, USA)).

data_processing:
Data were processed using Partek Genomics Suite 6.4 software and normalization according to RMA method.
Array control features have been filtered out.

label: biotin

source_name: Rhabdo - anti-miR-22, halved kidney

label_protocol: RNA integrity was checked by analyzing on the 2100 Bioanalyzer (Agilent technologies, PA, USA). For the first and subsequent second strand cDNA synthesis 200 ng of total RNA was used and, also, poly-A Spike Controls (containing several B. subtilis genes, that are absent in eukaryotic samples) are added in the recommended dilution to achieve the final concentrations corresponding to the given RNA amount of 200 ng. During the following in vitro transcription reaction cRNA was obtained and used as starting material for the second cycle cDNA synthesis. The second cycle random-primed single strand DNA synthesis resulted in a product containing incorporated deoxyuridine at predefined ratios relative to thymidine, according to the manufacturers recommendation: WT Expression Plus Kit (Affymetrix Inc., Santa Clara, CA, USA). Subsequently, 5.5 μg of this generated single-strand DNA was fragmented with a combination of uracil DNA glucosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1) and then labeled. The biotinylated DNA was added to a hybridization cocktail for hybridization to the Mouse Clariom S Array, also containing 50 pM control oligonucleotide B2, eukaryotic hybridization controls (bioB, bioC, bioD, 1,5, 5; 25 pM respectively), accordingly to the manufacturer’s protocol (Hybridization Wash and Stain Kit, Affymetrix).

growth_protocol: Male C57BL/6N mice (10 weeks old, 25-28 g) from Janvier (France) had free access to standard rodent chow and drinking water. Up to 6 mice were housed per cage in 12-h day and night cycles.

extract_protocol: 24 h after glycerol injection, animals were euthanized by cervical dislocation under isoflurane narcosis, and kidneys were rapidly removed, halved, and snap frozen in liquid nitrogen. Halved mouse kidneys were ground into fine powder in liquid nitrogen. RNA was isolated using RNA-Bee (AMS Biotechnology (Europe) Ltd - Germany) according to the manufacturer’s instructions.

treatment_protocol: To induce rhabdomyolysis-related AKI, mice were set under isoflurane narcosis, and 50% glycerol was injected into the gastrocnemic muscle. For induction of mild AKI, glycerol was applied unilaterally at a dose of 0.05 ml/10 g of body weight. For induction of severe AKI, glycerol was applied bilaterally at a total dose of 0.07 ml/10 g of body weight. Drinking water was withheld for a total of 23 h, 19 h prior and 4 h after glycerol injection. Analgesic treatment consisted of IP carprofen (5 mg/kg, Rimadyl©, Pfizer, Germany) at the time point of glycerol injection, as well as 3 h later. Anti-miR-22 ( I-mmu-miR-22-3p, sequence 5’-3’ CTTCAACTGGCAGCT, Exiqon, Denmark) or mock molecules (I-mmu-miR-22-3p MM, sequence 5’-3’ CTACTACAGGCTGCT, Exiqon, Denmark) were dissolved in 0.9% saline, and injected SC at a dose of 20 mg/kg of body weight 24 h prior to glycerol injection. In control animals the complete protocol was performed, except for the glycerol injection. Blood samples were collected from the retromandibular plexus 24 h after glycerol injection, then animals were euthanized by cervical dislocation under isoflurane narcosis, and kidneys were rapidly removed, halved, and snap frozen in liquid nitrogen.

tag: strain

tag: gender

value: male

value: kidney

tag: disease state

value: AKI

tag: treatment

value: miR-22 inhibitor


title: h1met1_RNA_rep3


title: IEL1516_2


title: poly(A)-selection, jird, adult male, a, SRX1539740

description:
bmalayi_counts.txt
bmalayi_tpm.txt

source_name: B. malayi adult males taken from jirds

value: jird, adult male


title: wt_RNA_rep4

description:
processed_data_file: col_seedling.f.bw
processed_data_file: col_seedling.r.bw


title: wt_RNA_rep3


title: poly(A)-selection, vector, infective L3, b, SRX4676610

description:
bmalayi_counts.txt
bmalayi_tpm.txt

organism:
Brugia malayi
Aedes aegypti
Wolbachia endosymbiont of Brugia malayi

source_name: B. malayi infective L3 taken from A. aegypti

tag: aedes aegypti strain

value: black-eyed Liverpool

value: vector, infective L3


title: wt_RNA_rep2


title: poly(A)-depletion, jird, 4 dpi, a, SRX1539745

description:
wbm_counts.txt
wbm_tpm.txt


title: Rhabdo - anti-miR-22 3

description: AKI animals & miR-22 inhibitor


title: Rhabdo - anti-miR-22 6

description: AKI animals & miR-22 inhibitor


title: Rhabdo - anti-miR-22 4

description: AKI animals & miR-22 inhibitor


title: poly(A)-depletion, jird, embryo, b, SRX1539739

description:
wbm_counts.txt
wbm_tpm.txt


title: Rhabdo - anti-miR-22 5

description: AKI animals & miR-22 inhibitor


title: Rhabdo - anti-miR-22 2

description: AKI animals & miR-22 inhibitor


title: poly(A)-selection, vector, infective L3, a, SRX4676609

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: met1_RNA_rep1


title: Rhabdo - anti-miR-22 1

description: AKI animals & miR-22 inhibitor


title: Rhabdo - mock 5

description: AKI animals & control molecules

source_name: Rhabdo - mock, halved kidney

value: control


title: Rhabdo - mock 7

description: AKI animals & control molecules


title: wt_RNA_rep1


title: poly(A)-selection, vector, 8 dpi, b, SRX1539954

description:
bmalayi_counts.txt
bmalayi_tpm.txt
aaegypti_counts.txt
aaegypti_tpm.txt

source_name: B. malayi taken from A. aegypti 8 dpi

value: vector, 8 dpi


title: poly(A)-selection, jird, adult male, b, SRX1539737

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: h1met1_bisulfite_rep4

description:
processed_data_file: h1met1.bisulfite.CG.w50.gff
processed_data_file: h1met1.bisulfite.CHG.w50.gff
processed_data_file: h1met1.bisulfite.CHH.w50.gff

library_source: genomic

molecule: genomic DNA

extract_protocol:
gDNA for bisulfite sequencing was extracted with Dneasy plant mini kit according to manufacturer's protocol.
To construct bisulfite sequencing libraries, about 500 ng of purified gDNA was fragmented to roughly 100-1000 bp then purified using 1.2X volume of SPRI beads (Beckman Coulter, cat. No. A63881). Fragmented gDNA was end-repaired and ligated to HPLC/PAGE purified, cytosine-methylated Illumina adapters (Elim Biopharmaceuticals, Inc.). DNA was subjected to two rounds of bisulfite conversion according to manufacturer's protocol (Qiagen, cat. No. 59104). To remove self-ligated adapters, DNA was purified twice with 0.8X volume of SPRI beads. NEB next indexing primers were used to amplify bisulfite-converted libraries (New England BIolabs Inc. cat. No. E7335S). DNA fragments isolated for ChIP-, ChAP-, and DnaseI-sequencing were subjected to Illumina library construction as described in bisulfite sequencing library construction except for the two rounds of bisulfite conversion.


title: poly(A)-selection, vector, 8 dpi, a, SRX1539952


title: h1met1_bisulfite_rep3


title: poly(A)-depletion, jird, embryo, a, SRX1539736

description:
wbm_counts.txt
wbm_tpm.txt


title: Rhabdo - mock 6

description: AKI animals & control molecules


title: poly(A)-depletion, jird, adult male, a, SRX1539735

description:
wbm_counts.txt
wbm_tpm.txt


title: poly(A)-selection, vector, 4 dpi, a, SRX1539947

source_name: B. malayi taken from A. aegypti 4 dpi

value: vector, 4 dpi


title: poly(A)-selection, jird, adult female, b, SRX1539734

description:
bmalayi_counts.txt
bmalayi_tpm.txt

value: jird, adult female


title: Rhabdo - mock 2

description: AKI animals & control molecules


title: Rhabdo - mock 4

description: AKI animals & control molecules


title: poly(A)-selection, vector, 18 hpi, b, SRX1539886

source_name: B. malayi taken from A. aegypti 18 hpi

value: vector, 18 hpi


title: Rhabdo - mock 1

description: AKI animals & control molecules


title: h1met1_bisulfite_rep2


title: poly(A)-selection, vector, 18 hpi, a, SRX1539876


title: h1met1_bisulfite_rep1


title: poly(A)-depletion, jird, adult male, b, SRX1539732

description:
wbm_counts.txt
wbm_tpm.txt

value: rRNA-, poly(A)-depletion


title: poly(A)-depletion, jird, adult female, b, SRX1539731

description:
wbm_counts.txt
wbm_tpm.txt


title: met1_bisulfite_rep3

description:
processed_data_file: met1.bisulfite.CG.w50.gff
processed_data_file: met1.bisulfite.CHG.w50.gff
processed_data_file: met1.bisulfite.CHH.w50.gff


title: met1_bisulfite_rep2


title: poly(A)-selection, jird, adult female, a, SRX1539730

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: wBm Agilent SureSelect, jird, adult female, b, SRX2508255

description:
wbm_counts.txt
wbm_tpm.txt


title: poly(A)-selection, vector, 8 dpbf, b, SRX5052526

description:
aaegypti_counts.txt
aaegypti_tpm.txt

organism: Aedes aegypti

source_name: A. aegypti 8 days post blood feeding

value: vector, 8 dpbf


title: met1_bisulfite_rep1


title: poly(A)-depletion, jird, adult female, a, SRX1539729

description:
wbm_counts.txt
wbm_tpm.txt


title: sham - anti-miR-22 3

description: control animals & miR-22 inhibitor

source_name: sham - anti-miR-22, halved kidney


title: sham - anti-miR-22 1

description: control animals & miR-22 inhibitor


title: poly(A)-selection, vector, 4 dpi, b, SRX1539949

value: poly(A)-enrichment


title: sham - anti-miR-22 4

description: control animals & miR-22 inhibitor


title: sham - anti-miR-22 2

description: control animals & miR-22 inhibitor


title: poly(A)-selection, vector, 8 dpbf, a, SRX5052525

description:
aaegypti_counts.txt
aaegypti_tpm.txt


title: poly(A)-depletion, jird, adult female, d, SRX1539727

description:
wbm_counts.txt
wbm_tpm.txt


title: sham - anti-miR-22 5

description: control animals & miR-22 inhibitor


title: sham - mock 5

description: control animals & control molecules

source_name: sham - mock, halved kidney


title: wt_bisulfite_rep4

description:
processed_data_file: col.bisulfite.CG.w50.gff
processed_data_file: col.bisulfite.CHG.w50.gff
processed_data_file: col.bisulfite.CHH.w50.gff

value: 2 week old seedlings


title: poly(A)-selection, vector, 18 hpbf, b, SRX5052524

description:
aaegypti_counts.txt
aaegypti_tpm.txt

source_name: A. aegypti 18 hours post blood feeding

value: vector, 18 hpbf


title: poly(A)-selection, vector, 4 dpbf, b, SRX5052522

description:
aaegypti_counts.txt
aaegypti_tpm.txt

source_name: A. aegypti 4 days post blood feeding

value: vector, 4 dpbf


title: poly(A)-selection, vector, 18 hpbf, a, SRX5052523

description:
aaegypti_counts.txt
aaegypti_tpm.txt


title: wt_bisulfite_rep2

source_name: 2 week old seedlings


title: poly(A)-selection, vector, 4 dpbf, a, SRX5052521

description:
aaegypti_counts.txt
aaegypti_tpm.txt


title: poly(A)-depletion, jird, adult female, c, SRX1539589

description:
wbm_counts.txt
wbm_tpm.txt


title: wt_bisulfite_rep1


title: poly(A)-selection, jird, adult female, c, SRX1539085

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: poly(A)-selection, jird, adult female, d, SRX1539707

description:
bmalayi_counts.txt
bmalayi_tpm.txt


title: Control larvae 1

status: Public on Nov 19 2019

city: London

first: Vincenzo

last: Torraca

state: London

address: Keppel street

institute: LSHTM

data_processing:
Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1.
Conversion of the bcl2 file to de-multiplexed gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina.
Quality and adapter trimming of fastq files was performed with trimmomatic-0.36.jar SE using parameters: -phred33;ILLUMINACLIP:adapter:2:30:10;SLIDINGWINDOW:4:15;LEADING:3;TRAILING:3;MINLEN:30
Mapping of the reads to the genomes was performed with bowtie2 using parameter --local
Read counting was performed with featureCounts version 1.5.0-p1
Genome_build: GRCz11 (Danio rerio), ASM28371v1  (S. sonnei 53G)
Supplementary_files_format_and_content: tab-separated values (TSV) files include geneID, gene name, gene description, log2foldchange (Deseq2), pvalue (Deseq2), padj (Deseq2), chromosome name, position (start, end and strand), length, reads and RPKM per each sample

source_name: pool of 20 zebrafish larvae

growth_protocol: Larvae were obtained by natural spawning and maintained at 28.5C until 3 days post fertilisation in 0.5xE2 medium (7.5 mM NaCl, 0.25 mM KCl, 0.5 mM MgSO4, 75 µM KH2PO4,  25 µM Na2HPO4, 0.5 mM CaCl2, 0.35 mM NaHCO3). For injections, larvae were then anaestesised in 0.5xE2 medium supplemented with 200 ug/ml tricaine, and injected with bacterial resuspension buffer alone (2% polyvinylpyrrolidone, 0.5% phenol red in phosphate buffer saline). Injected larvae were then returned in E2 medium without anesthetic and maintained at 28.5C for 24h before collection.

extract_protocol:
Samples were snap frozen at -80°C, then 100 μl of RNA protect bacteria reagent (Qiagen) was added, followed by mechanical trituration with a pestle blender. Samples were supplemented with 100 μl of 30 mM Tris-HCl/1 mM EDTA solution at pH = 8, 33 μl of 50 mg/ml lysozyme (Thermo Scientific), 33 μl of proteinase K >600 U/ml (Thermo Scientific) and shaken for 20 min RT. Lysis was completed by adding 700 μl of RTL buffer (Qiagen), 3 μl of 1 M dithiothreitol (Sigma-Aldrich) and mechanical disruption. Undigested debris were spun down 3 min 10000 rpm and the supernatant was supplemented with 500 μl of 100% ethanol prior loading onto RNeasy mini columns (Qiagen). From this step onwards, the manufacturer’s guidelines were followed for RNA purification. RNA quality and integrity were assessed by using NanoDrop and Non-denaturing agarose gel electrophoresis. For further quality check, RNA sequencing, library construction and reads count, samples were outsourced to Vertis Biotechnologie AG (Freising, Germany). Bacterial and host mRNA were enriched prior library preparation by using Ribo-Zero Gold rRNA Removal Kit (Epidemiology, Illumina, San Diego, California).
The rRNA depleted RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase . The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool was size fractionated in the size range of 200 – 550 bp using a preparative agarose gel. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina. The cDNA pools were sequenced on an Illumina NextSeq 500 system using 75 bp read length.

value: AB

tag: incubation temperature

tag: collection point

value: 24 hours post injection


title: Control larvae 3


title: Control larvae 2

description: ssonnei_processed_data.tsv, zebrafish_processed_data.tsv


title: DMSO Day14

city: shanghai

first: Tingting

last: Liu

address: 320,yueyang road

country: China

institute: insititute of health sciences

data_processing:
Library strategy: GeCKO library screen
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to GeCKO V2 Human library A sgRNA sequences using MAGeCK 0.5.7 with parameters mageck count --fastq -l -n
Normalization measurements were generated using MAGeCK 0.5.7 with parameters mageck count -k --norm-method median -n
Differential analysis between two groups was proceeded by MAGeCK 0.5.7 with parameters mageck mle -k --day0-label -n --thread --permutation-round
Genome_build: hg19

organism: Homo sapiens

growth_protocol: Cells were maintained in either RPMI 1640 with 10% fetal bovine serum and 1% penicillin streptomycin . The condition of incubator for cells culture was maintained at 37 °C, 5% CO2. Cells were passaged using 0.25% Trypsin-EDTA.

extract_protocol:
The genomic DNA of the three groups (DMSOD0, DMSOD14, RTXD14) were extracted with a Blood & Cell Culture Midi kit,PCR was performed in two steps for each group. The production of the second PCR was purified by gel extraction (Qiagen, Cat.No.20051) and sequenced by Illumina HiSeq X Ten.
GeCKO libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSODay0 group was treated with DMSO for 14 days, RTXDay14 group was treated with 10nM RTX for 14 days.

tag: cell line

value: gastric cancer

value: DMSO Day14


title: NUGC3_Scramble [X1.T.SC.DOX.R1]

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

data_processing:
Sequenced reads were aligned to Ensemble database with STAR.
Gene expression values were normalized to obtain RPKM values using RSEM.
Differentially expressed genes were analysed using GSEA.
Genome_build: Ensemble
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample .

extract_protocol:
After cells were transfected with Scramble or shNIPBL, the cells were harvesed and lysed  in Trizol reagent and total RNA was eztracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gastric cancer cell line

value: scramble


title: NUGC3_shNIPBL#1 [X2.T.N.1.DOX]

value: NIPBL-knockdown


title: NUGC3_shNIPBL#7 [X3.T.N.7.DOX]


title: NUGC3_Scramble [X1.T.SC.DOX]


title: sham - mock 3

description: control animals & control molecules

value: male

value: kidney

value: control


title: RTX Day14

value: 10nM RTX for 14 days


title: DMSO Day0

value: DMSO Day0


title: wzdN [RNA-Seq]

city: Ningbo

first: Jiaxin

last: Ge

state: Zhejiang

address: 247 Renmin Road

institute: The Affiliated Hospital of Medical School, Ningbo University

description: all.counts.exp.txt

data_processing:
mRNA: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
mRNA: Hisat2 2.0.4 mapping to reference genome
mRNA: count counting
miRNA: We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) a)10% base quality <15 b) 13% base quality <20 c) 15bp < read length < 30bp.
miRNA: Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo Sapiens miRNA database and GRCH38.p10 genome.
miRNA: count counting
Genome_build:  hg19_GRCh38 / miRBase 21.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: colorectal pericarcinomatous tissue

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: rectum

value: 49 years


title: gzyN [RNA-Seq]

description: all.counts.exp.txt

value: colon

value: 70 years


title: wzdC [RNA-Seq]

description: all.counts.exp.txt

source_name: colorectal cancer tissue

tag: tumor stage

value: T4N1bM0 (ⅢB)


title: sham - mock 2

description: control animals & control molecules


title: gzyC [RNA-Seq]

description: all.counts.exp.txt

value: T3N1M0 (ⅢB)


title: N454750 [RNA-Seq]

description: all.counts.exp.txt

value: 54 years


title: C454750 [RNA-Seq]

description: all.counts.exp.txt


title: sham - mock 1

description: control animals & control molecules


title: HET-718

city: Melbourne

first: Joanne

last: Wong

state: VIC

address: Kingsbury Drive

department: PAM

country: Australia

institute: La Trobe University

data_processing:
Raw RNA-sequencing data were quality assessed using fastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Adapter and low-quality fragments were removed using trimmimatic (v0.32)
Clean reads were  mapped to the Mus musculus genome (assembly GRCm38.p6) by HISAT2 (v2.0.5)
Alignment quality control was performed using RSeQC (v2.6.4)
Expression of each gene was determined by the featureCounts function in subread (v1.4.6p5)
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: CSV file contaisn transcripts per kilobase million values for each sample

source_name: Epididymis

extract_protocol:
Epididymides were harvested and teased apart in cold phosphate-buffered saline (PBS) and  rinsed in two changes of PBS to remove sperm. Samples were  homogenised using a mortar and pestle in TRIzol Reagent (Invitrogen, Carlsbad, CA, USA), according to manufacturer instructions. Total RNA was treated with DNase using  TURBO DNA-free kit (Invitrogen) and  purified using  Zymo RNA Clean & Concentrator-25 kit (Zymo Research Corporation, Irvine, CA, USA), according to manufacturer instructions. Libraries were constructed using 2ug purified RNA and the Illumina TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA) as per manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brown Swiss

value: Epididymis

value: 7 weeks

tag: genotype

value: Plag1 -/+


title: KO-696

value: Plag1 -/-


title: KO-738


title: KO-739


title: KO-694


title: KO-695


title: HET-735


title: HET-715


title: HET-693


title: HET-692


title: WT-719

value: Wild type


title: WT-726


title: WT-723


title: WT-720


title: Rhabdo - mock 3

description: AKI animals & control molecules

value: male

value: kidney

value: AKI


title: WT-709


title: C57BL6/N 0.08 ppm Se rep3

city: Honolulu

first: Lucia

last: Seale

state: Hawaii

address: 651 Ilalo st. BSB222

institute: University of Hawaii

data_processing:
FASTQ files were explored using FASTQC prior cleaning.
Reads were cleaned by trimming adapters and bases with Phred quality score less than 20 from both 3’ and 5’ ends using Cutadapt
Cleaned reads were imported into Partek Flow software (Partek Inc., St. Louis, MO, USA) to align against mm10 mouse reference genome using STAR
Quantify to annotation model using Partek E/M
DESeq2 Bioconductor package  was used for the differential gene expression and genes with FDR-adjusted p-values less than 005 were called differentially expressed
Genome_build: mm10
Supplementary_files_format_and_content: Excel files containing raw count matrix and DESeq results

source_name: liver

extract_protocol:
Total RNA was extracted using the Qiagen AllPrep DNA/RNA kit (Qiagen) disrupted with disposable probes using the Qiagen TissueRuptor.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice of two genotypes were fed for at least 8 weeks with 12% kcal diets containing either 0.08 or 0.25 ppm of sodium selenite.

tag: Sex

tag: dietary selenium intake

value: 0.08 ppm Se


title: Scly KO 0.25 ppm Se rep3

value: Scly KO

value: 0.25 ppm Se


title: C57BL6/N 0.25 ppm Se rep1


title: Scly KO 0.08 ppm Se rep1


title: Scly KO 0.25 ppm Se rep2


title: C57BL6/N 0.08 ppm Se rep2


title: C57BL6/N 0.25 ppm Se rep3


title: Scly KO 0.25 ppm Se rep1


title: C57BL6/N 0.25 ppm Se rep2


title: Scly KO 0.08 ppm Se rep2


title: C57BL6/N 0.08 ppm Se rep1


title: Tumor_UTR5

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

description: RNA, rRNA depleted

data_processing:
Reads were mapped against the mouse genome (GRCm38) and mouse rRNA sequences using ContextMap 2.7.9 with BWA as internal alignment program.
Read counts per gene (from Gencode version 16) were calculated using the featureCounts program from the subread package (v1.4.6-p3).
Genome_build: GRCm38
Supplementary_files_format_and_content: counts

source_name: Bulk Tumor

growth_protocol: Not applicable

extract_protocol:
Single cell suspension of tumor and spleens was generated, CD11b+ cells were enriched by MACS sorting, live MDSC populations (PMN-MDSC= CD11b+Ly6CloLy6G+; M-MDSC =CD11b+Ly6ChiLy6G-) were isolated by FACS sorting. Bulk tumor samples were directly lysed in QIAzol Lysis buffer. RNA was extrated using the QIAzol Lysis buffer together with the Qiagen RNeasy Kit.
Library for RNA sequencing was prepared using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico-Input Mammalian (TaKaRa). In brief, up to 10 ng RNA was fragmented for 4 min at 94°C, followed by first-strand cDNA synthesis. Next, Illumina Adapters and Indexes were added. Subsequently, RNA sequencing library was isolated using AMPure beads and ribosomal RNA was depleted using ZapRv2 and R-Probes v2. Finally, RNAseq library was amplified in 13 cycles und isolated using AMPure beads.

treatment_protocol: Mice were treated i.v. at day 18 and 20 after T110299 tumor induction with either poly(I:C)-PEI (50µg Poly(I:C) HMW vaccigrade complexed with in vivo-jetPEI® at N/P ratio of 6) or glucose as control

tag: cell

value: tumor

tag: organ

value: untreated


title: Tumor_UTR2

description: RNA, rRNA depleted


title: Spl_M_PIC8

description: RNA, rRNA depleted

source_name: splenic M-MDSC

value: M-MDSC

value: spleen


title: Tu_M_PIC7

description: RNA, rRNA depleted

source_name: Tumor-derived M-MDSC


title: Tumor_UTR1

description: RNA, rRNA depleted


title: Scly KO 0.08 ppm Se rep3


title: Spl_M_PIC7

description: RNA, rRNA depleted


title: Spl_PMN_PIC7

description: RNA, rRNA depleted

source_name: splenic PMN-MDSC

value: PMN-MDSC


title: Tu_M_PIC8

description: RNA, rRNA depleted


title: Spl_PMN_PIC8

description: RNA, rRNA depleted


title: Tu_PMN_UTR6

description: RNA, rRNA depleted

source_name: Tumor-derived PMN-MDSC


title: Tu_PMN_PIC7

description: RNA, rRNA depleted


title: Spl_PMN_UTR6

description: RNA, rRNA depleted


title: Spl_M_UTR6

description: RNA, rRNA depleted


title: Tu_M_UTR5

description: RNA, rRNA depleted


title: Tu_PMN_PIC3

description: RNA, rRNA depleted


title: Spl_M_UTR5

description: RNA, rRNA depleted


title: Spl_PMN_UTR5

description: RNA, rRNA depleted


title: Tu_M_PIC3

description: RNA, rRNA depleted


title: Tu_PMN_UTR5

description: RNA, rRNA depleted


title: Tumor_UTR6

description: RNA, rRNA depleted


title: Spl_M_PIC4

description: RNA, rRNA depleted


title: Spl_PMN_PIC3

description: RNA, rRNA depleted


title: Tu_PMN_PIC8

description: RNA, rRNA depleted


title: Spl_M_PIC3

description: RNA, rRNA depleted


title: sham - mock 4

description: control animals & control molecules

tag: tissue

value: control


title: Tu_M_UTR6

description: RNA, rRNA depleted


title: Tu_M_UTR2

description: RNA, rRNA depleted


title: wt_bisulfite_rep3

value: 2 week old seedlings


title: Spl_M_UTR2

description: RNA, rRNA depleted


title: Tu_PMN_UTR2

description: RNA, rRNA depleted


title: Tu_PMN_UTR1

description: RNA, rRNA depleted


title: Spl_PMN_UTR1

description: RNA, rRNA depleted


title: Spl_M_UTR1

description: RNA, rRNA depleted


title: wzdC [miRNA-Seq]

description: miRNA.All.Counts.exp.txt

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA libraries were prepared for sequencing using standard IonPronton protocols

value: rectum

value: T4N1bM0 (ⅢB)

tag: age

value: 49 years


title: N454750 [miRNA-Seq]

description: miRNA.All.Counts.exp.txt

value: 54 years


title: Tu_M_UTR1

description: RNA, rRNA depleted


title: Tu_PMN_PIC4

description: RNA, rRNA depleted


title: C454750 [miRNA-Seq]

description: miRNA.All.Counts.exp.txt

value: T3N1M0 (ⅢB)


title: Tu_M_PIC4

description: RNA, rRNA depleted


title: gzyC [miRNA-Seq]

description: miRNA.All.Counts.exp.txt

value: colon

value: 70 years


title: wzdN [miRNA-Seq]

description: miRNA.All.Counts.exp.txt


title: gzyN [miRNA-Seq]

description: miRNA.All.Counts.exp.txt


title: 9-c

city: Linköping

first: Rada

last: Ellegård

state: Ostergotlands Lan

address: Vallmogatan 16

country: Sweden

institute: Linköping University

data_processing:
Trimmomatic
STAR
featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt raw counts

source_name: monocyte derived dendritic cells

extract_protocol:
Isolate II RNA Micro Kit (Bioline, UK)
Ovation® RNA-Seq System V2 | NuGEN

tag: cell type

value: monocyte derived dendritic cells

tag: condition

tag: donor

value: c


title: 9-d

value: d


title: 6-e

value: e


title: 9-a

value: a


title: 6-c


title: 6-d


title: 9-b

value: b


title: 9-e


title: 6-a


title: 5-e

value: CHIV


title: 6-b


title: 5-d


title: Spl_PMN_UTR2

description: RNA, rRNA depleted

value: PMN-MDSC

value: spleen

value: untreated


title: 5-a


title: 5-c


title: 3-e

value: HIV


title: 3-d


title: 1-e

value: mock


title: 3-a


title: 3-b


title: 1-c


title: 3-c


title: 1-b


title: HT_48

city: Parkville

first: Ali

last: Motazedian

state: Victoria

address: Royal Children's Hospital

department: Stem Cell Technology

institute: Murdoch Children's Research Institute

data_processing:
Individual fastq files were aligned to the reference genome (GRCh38 assembly and ENSEMBL version 91) with Rsubread 1.20.6 with default settings in R version 3.2.2. Reads were summarised from bam files to counts with the featureCounts library within Rsubread 1.20.6.
Genome_build: GRCh38.91
Supplementary_files_format_and_content: raw_gene_counts_hg38_ensembl91 is a tab delimited text file, which contains raw gene counts for individual samples (columns), as well as "Gene.stable.ID", "Gene.description", "Gene.name", "NCBI.gene.ID" and "gene.length" for each gene (rows).
Supplementary_files_format_and_content: *.tabular.txt: Tabular files generated from RNA STAR using modified gencode.v30.chr_patch_hapl_scaff.annotation.gtf file containing GFP gene annotation. Each file contains column 1: gene ID, column 2: counts for unstranded RNA-seq, column 3: counts for the 1st read strand aligned with RNA , column 4: counts for the 2nd read strand aligned with RNA.

source_name: human thymus

growth_protocol: Pluripotent stem cell lines were differentiated as embryoid bodies (EBs) for 8 days in presence of appropriate supplements. The EBs were then transferred onto Corning transmembranes to grow in air liquid interface system until the end of experiments.

extract_protocol:
Desired populations were purified using BD FACSAria FUSION. Total RNA extraction of FACS purified populations was performed using TRIzol reagent (Thermofisher) according to manufacturer’s guidelines.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: experiment #

tag: differentiation day

tag: representative population

value: DP

value: human thymus

tag: sort parameters


title: 1-a


title: HT_483


title: iPS_R_5

source_name: human induced pluripotent stem cells

value: human induced pluripotent stem cells


title: iPS_3490_5

value: Endothelium


title: iPS_34_4

value: Blood


title: iPS_3490_4


title: iPS_34_5


title: iPS_34_2


title: 5-b

value: monocyte derived dendritic cells


title: iPS_34_1


title: H9_R_1

source_name: human embryonic stem cells

value: human embryonic stem cells


title: iPS_3490_1


title: H9_R_2


title: iPS_R_1


title: H9_3490_1


title: iPS_R_4


title: H9_34_1


title: iPS_4R_4


title: 1-d

value: d


title: iPS_R_2


title: iPS_57R_4


title: iPS_neg_4


title: iPS_48R_4


title: iPS_57_3

value: DN


title: iPS_48R_3


title: iPS_57R_3


title: iPS_neg_3


title: H9_34_2


title: iPS_48R_2


title: iPS_4R_2


title: iPS_57R_2


title: iPS_57_2


title: iPS_neg_2


title: iPS_57R_1


title: iPS_48R_1


title: iPS_57_1


title: H9_48R_4


title: H9_57R_4


title: iPS_57_4


title: iPS_neg_1


title: H9_57R_3


title: iPS_4R_3


title: H9_neg_4


title: H9_4R_4


title: H9_4R_3


title: H9_57_4


title: H9_48R_2


title: H9_57_3


title: H9_neg_3


title: H9_4R_2


title: H9_57_2


title: H9_57R_2


title: H9_48R_1


title: H9_neg_2


title: H9_57_1


title: H9_57R_1


title: H9_4R_1


title: iPS_4R_1


title: H9_neg_1


title: H9_48R_3


title: RSV_vehicle_7d_M_67

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

data_processing:
Reads were de-multiplexed with the Illumina pipeline. Raw reads were aligned to a reference FASTA file that contains a curated list of transcripts (RefSeq, transcripts as of 2013). Alignment was done with BWA (Burrows-Wheeler Aligner) and reads per million (RPM) values were created from the sequence alignment map (SAM) output file
Messenger RNAs less than 200 bp were eliminated from the analysis.
Genome_build: transcripts as of March 2013, plus ERCC spike in probes and mitochondrial sequences.  File name included in submission is "mouse_refgu_ERCC.seq"
Supplementary_files_format_and_content: text file containing normalized (reads per million=RPM) expression values for genes 200 base pairs and longer

source_name: lung

growth_protocol: BALB/c mice were mock treated or infected with 5.5x10^5 RSV A2 with or without 3 mg/kg dexamethasone.  During scheduled takedowns on day 5 or 7, a left lung specific BAL performed by first tying off the upper right lobe (3x0.2 ml sterile saline). After BAL the upper right lobe was aseptically removed into a 1.7ml Eppendorf tube containing 0.4ml RNA later, weighed, and placed on ice.

extract_protocol:
RNA was extracted using Qiagen RNeasy 96 Universal Tissue Kit (Cat #74881), where samples were homogenized in QIAzol followed by Chloroform extraction and ethanol precipitation. Then the samples were then purified using the columns contained in the kit using the manufacturer's protocol.
500 ng total RNA was used to make Illumina libraries using the TruSeq stranded kit

tag: strain

value: BALB/c

value: lung

tag: infection

value: RSV

tag: time point

value: 7 days


title: RSV_vehicle_7d_M_66

treatment_protocol: BALB/c mice were mock treated or infected with 5.5x10^5 RSV A2 with or without 3 mg/kg dexamethasone.  During scheduled takedowns on day 5 or 7, a left lung specific BAL performed by first tying off the upper right lobe (3x0.2 ml sterile saline). After BAL the upper right lobe was aseptically removed into a 1.7ml Eppendorf tube containing 0.4ml RNA later, weighed, and placed on ice.


title: RSV_vehicle_7d_M_65


title: RSV_vehicle_5d_M_20

value: 5 days


title: RSV_vehicle_5d_M_21


title: RSV_dex_7d_M_77

tag: treatment

value: Dexamethasone, 3 mg/kg


title: RSV_dex_7d_M_76


title: Day7 10Gy rep12

city: New York

first: Sally

last: Amundson

state: NY

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays 4X44K v2 (G4846A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers or not significantly above background were excluded.

source_name: whole blood_Day7 10Gy

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mice were housed under standard vivarium conditions, and all procedures were conducted under an approved IACUC protocol.

extract_protocol: Mice were euthanized at 1, 2, 3, 5 or 7 days after irradiation. Blood was obtained via cardiac puncture and immediately added to a tube containing PAXgene Blood RNA stabilization and lysis solution at a ratio of 1:5 (blood:solution) and mixed. RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment, followed by globin reduction using GLOBINclear-Mouse/Rat.

treatment_protocol: Mice at 8-10 weeks of age were exposed in the early afternoon to total body radiation doses of 0, 1.5, 3, 6, or 10 Gy using an AECL Gammacell-40 137Cs gamma-ray source at a dose rate 1.05 Gy/ min.

tag: Sex

value: male

value: 8-10 weeks

value: Day7 10Gy

value: whole blood


title: RSV_dex_7d_M_75


title: Day7 3Gy rep6

source_name: whole blood_Day7 3Gy

value: Day7 3Gy


title: RSV_vehicle_5d_M_23


title: RSV_dex_5d_M_32


title: Day7 3Gy rep2


title: Day7 1.5Gy rep10

source_name: whole blood_Day7 1.5Gy

value: Day7 1.5Gy


title: RSV_dex_5d_M_30


title: RSV_dex_5d_M_26


title: Day7 3Gy rep3


title: Day7 10Gy rep5


title: Day7 3Gy rep10


title: Day7 10Gy rep7


title: Day7 1.5Gy rep9


title: mock_vehicle_7d_M_53

value: mock


title: Day7 3Gy rep9


title: Day7 10Gy rep10


title: Day7 10Gy rep6


title: Day7 10Gy rep8


title: Day7 3Gy rep5


title: Day7 3Gy rep7


title: Day7 10Gy rep9


title: Day7 3Gy rep1


title: Day7 10Gy rep3


title: Day7 3Gy rep4


title: Day7 3Gy rep8


title: Day7 1.5Gy rep7


title: Day7 1.5Gy rep8


title: Day7 1.5Gy rep6


title: Day7 1.5Gy rep5


title: mock_vehicle_5d_M_06


title: mock_vehicle_5d_M_08


title: mock_vehicle_7d_M_52


title: mock_vehicle_7d_M_55


title: Day7 1.5Gy rep4


title: Day7 1.5Gy rep3


title: mock_vehicle_5d_M_04


title: Day7 Control rep7

source_name: whole blood_Day7 Control

value: Day7 Control


title: Day7 1.5Gy rep2


title: cell_overexpression_rep2

city: shenyang

first: Longyang

last: Jiang

state: liaoning

address: No.77 Puhe Road, Shenyang North New Area, Shenyang,      Liaoning Province, P.R. China

institute: China Medical Univisity

description: Gene expression after transfected lncRNA-SPRY4-IT1 overexpression vector in HCT116

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HCT116, lncRNA-SPRY4-IT1 overexpression vector, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cell was cultured with McCoy's 5a, 10% fetal bovine serum, 5% CO2.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies) and RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's recommendations.

treatment_protocol: The colorectal cancer cell line HCT116 transfected with lncRNA-SPRY4-IT1 overexpression or control vector. The cultures were incubated for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: transfection

value: overexpression


title: Day7 Control rep10


title: Day7 Control rep5


title: cell_overexpression_rep3

source_name: HCT116, lncRNA-SPRY4-IT1 overexpression vector, replicate 3


title: cell_control_rep3

description: Gene expression after transfected control vector in HCT116

source_name: HCT116, negative control vector, replicate 3

value: negative control


title: Day7 1.5Gy rep1


title: Day7 Control rep9


title: cell_overexpression_rep1

source_name: HCT116, lncRNA-SPRY4-IT1 overexpression vector, replicate 1


title: Day7 Control rep8


title: Day7 6Gy rep3

source_name: whole blood_Day7 6Gy

value: Day7 6Gy


title: Day7 Control rep1


title: Day7 Control rep4


title: cell_control_rep2

source_name: HCT116, negative control vector, replicate 2


title: cell_control_rep1

source_name: HCT116, negative control vector, replicate 1


title: Day7 Control rep3


title: Day7 6Gy rep1


title: Day7 6Gy rep2


title: Day7 6Gy rep4


title: Day7 Control rep2


title: Day7 6Gy rep10


title: Day7 Control rep6


title: Intestine, feed with fish oil, fish 69

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with Agilent microarray scanner

data_processing: Global normalization was performed by equalizing the mean intensities of all microarrays. The individual values for each feature were divided to the mean value of all samples and expression ratios (ER) were calculated. Log2-ER were normalized with the locally weighted non-linear regression (Lowess)

organism: Salmo salar

source_name: intestine

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was grown in tanks at aquaculture research station

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

value: intestine


title: Intestine, feed with fish oil, fish 68


title: Intestine, feed with fish oil, fish 67


title: Day7 6Gy rep8


title: Intestine, feed with fish oil, fish 64


title: Intestine, feed with fish oil, fish 40


title: Intestine, feed with fish oil, fish 41


title: Day7 6Gy rep9


title: Intestine, feed with fish oil, fish 6


title: Intestine, feed with fish oil, fish 39


title: Intestine, feed with fish oil, fish 38


title: Day7 6Gy rep7


title: Day5 6Gy rep14

source_name: whole blood_Day5 6Gy

value: Day5 6Gy


title: Day5 6Gy rep11


title: Day5 6Gy rep6


title: Day5 6Gy rep12


title: Intestine, feed with fish oil, fish 5


title: Intestine, feed with fish oil, fish 2


title: Intestine, feed with algae biomass, fish 60


title: Intestine, feed with algae biomass, fish 54


title: Day5 6Gy rep8


title: Day5 6Gy rep3


title: Day7 6Gy rep5


title: Day5 6Gy rep9


title: Day5 6Gy rep13


title: Intestine, feed with algae biomass, fish 51


title: Day7 6Gy rep6


title: Intestine, feed with fish oil, fish 8


title: Day5 6Gy rep5


title: Intestine, feed with algae biomass, fish 49


title: Intestine, feed with algae biomass, fish 35


title: Day5 3Gy rep10

source_name: whole blood_Day5 3Gy

value: Day5 3Gy


title: Intestine, feed with algae biomass, fish 30


title: Day5 6Gy rep2


title: Intestine, feed with algae biomass, fish 13


title: Intestine, feed with algae biomass, fish 15


title: Intestine, feed with algae biomass, fish 29


title: Intestine, feed with fish oil, fish 20


title: Day5 3Gy rep7


title: Liver, feed with fish oil, fish 69

source_name: liver

value: liver


title: Liver, feed with fish oil, fish 64


title: Day5 3Gy rep8


title: Liver, feed with fish oil, fish 68


title: Liver, feed with fish oil, fish 67


title: Liver, feed with fish oil, fish 41


title: Day5 3Gy rep1


title: Intestine, feed with algae biomass, fish 33


title: Day5 3Gy rep5


title: Day5 3Gy rep6


title: Liver, feed with fish oil, fish 40


title: Intestine, feed with algae biomass, fish 22


title: Day5 1.5Gy rep8

source_name: whole blood_Day5 1.5Gy

value: Day5 1.5Gy


title: Day5 3Gy rep4


title: Day5 3Gy rep2


title: Day5 1.5Gy rep10


title: Day5 3Gy rep3


title: Day5 10Gy rep17

source_name: whole blood_Day5 10Gy

value: Day5 10Gy


title: Day5 1.5Gy rep9

value: male


title: Day5 1.5Gy rep7

value: 8-10 weeks


title: Day5 10Gy rep16


title: Day5 10Gy rep13


title: Liver, feed with fish oil, fish 39


title: Day5 10Gy rep9


title: Day5 10Gy rep12


title: Liver, feed with fish oil, fish 38


title: Liver, feed with fish oil, fish 6


title: Day5 10Gy rep10


title: Liver, feed with fish oil, fish 5


title: Liver, feed with fish oil, fish 8


title: Liver, feed with algae biomass, fish 51


title: Liver, feed with algae biomass, fish 60


title: Liver, feed with algae biomass, fish 30


title: Liver, feed with algae biomass, fish 54


title: Liver, feed with fish oil, fish 2


title: Liver, feed with algae biomass, fish 33


title: Day5 10Gy rep8


title: Liver, feed with algae biomass, fish 35


title: Liver, feed with algae biomass, fish 22


title: Liver, feed with algae biomass, fish 29


title: Day5 1.5Gy rep6


title: Liver, feed with algae biomass, fish 20


title: Day5 1.5Gy rep2


title: Day5 1.5Gy rep4


title: Day5 1.5Gy rep3


title: Liver, feed with algae biomass, fish 49


title: Day5 Control rep9

source_name: whole blood_Day5 Control

value: Day5 Control


title: Day5 1.5Gy rep1

value: whole blood


title: Day5 1.5Gy rep5


title: Day5 Control rep8


title: Day5 Control rep10


title: Day5 Control rep11


title: Day5 Control rep6


title: Day5 Control rep5


title: Liver, feed with algae biomass, fish 13


title: Day5 Control rep7


title: Liver, feed with algae biomass, fish 15


title: Day5 Control rep2


title: Day5 Control rep3


title: Day3 1.5Gy rep10

source_name: whole blood_Day3 1.5Gy

value: Day3 1.5Gy


title: Day3 1.5Gy rep9


title: Day5 10Gy rep6


title: liver_UN-TU_HFD_30

city: Hamamatsu

first: Hiroaki

last: Itoh

address: #1-20-1 Handayama, Higashi-ku

department: Obstetrics and Gynecology

country: Japan

institute: Hamamatsu University School of Medicine

description: gene expression data at 22 weeks; liver tissue from UN after postnatal HFD with TUDCA

hyb_protocol: Hybridization was done using Mouse Gene 2.1 ST array strip kit materials • Heat cocktails at 96° for 10 minutes, then 45° for 5 minutes centrifuge at max speed for 5 minute • Transfer 120μl of hyb solution to each array and cover with hybridization strip. • Hybridize 20 hours at 48° at 60rpm•  wash was done according to the manufacturer protocol.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were analyzed with Expression console and Transcriptome console version 3 using Affymetrix default analysis settings and background control and normalization were done accordingly. Statistical analysis was performed using one-way ANOVA (unpaired) among two groups.

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Liver tissue was dissected at 9, 17 and 22 weeks from our specified mouse model.

extract_protocol: Total RNA extraction from 100 mg of liver tissue and was performed according to the manufacturer's instructions (The RNeasy Lipid Tissue Mini Kit (cat. no. 74804))

tag: in utero condition

value: undernourished

tag: diet

value: postnatal HFD with TUDCA

tag: gender

value: Male

value: Liver

value: 22 weeks


title: Day5 10Gy rep7

tag: age

tag: tissue


title: liver_UN-Veh_HFD_24

description: gene expression data at 22 weeks; liver tissue from UN after postnatal HFD without TUDCA

value: postnatal HFD without TUDCA


title: liver_UN-TU_HFD_29

source_name: liver tissue from UN after postnatal HFD with TUDCA


title: Day5 10Gy rep4


title: liver_UN-Veh_HFD_25

source_name: liver tissue from UN after postnatal HFD without TUDCA


title: Day5 3Gy rep9


title: Day3 10Gy rep1

source_name: whole blood_Day3 10Gy

value: Day3 10Gy


title: liver_NN-TU_HFD_21

description: gene expression data at 22 weeks; liver tissue from NN after postnatal HFD with TUDCA

value: normal nutrition


title: Day5 Control rep4


title: liver_NN-TU_HFD_20

source_name: liver tissue from NN after postnatal HFD with TUDCA


title: Day3 1.5Gy rep7


title: liver_UN-Veh_HFD_26


title: liver_UN-TU_HFD_27


title: Day3 1.5Gy rep8


title: liver_UN-Veh_HFD_23


title: Day3 6Gy rep11

source_name: whole blood_Day3 6Gy

value: Day3 6Gy


title: Day3 6Gy rep9


title: Day3 6Gy rep10


title: liver_NN-Veh_HFD_17

description: gene expression data at 22 weeks; liver tissue from NN after postnatal HFD without TUDCA


title: liver_NN-Veh_HFD_18

source_name: liver tissue from NN after postnatal HFD without TUDCA


title: liver_NN-TU_HFD_19


title: liver_NN-Veh_HFD_16


title: liver_UN_HFD_14

description: gene expression data at 17 weeks; liver tissue from UN after postnatal HFD

value: postnatal HFD

value: 17 weeks


title: Day3 6Gy rep2


title: Day3 6Gy rep1


title: Day3 3Gy rep15

source_name: whole blood_Day3 3Gy

value: Day3 3Gy


title: liver_UN-TU_HFD_28


title: Day3 6Gy rep5

value: male


title: liver_UN_HFD_13

source_name: liver tissue from UN after postnatal HFD


title: Day3 6Gy rep4

value: 8-10 weeks


title: liver_NN_HFD_10

description: gene expression data at 17 weeks; liver tissue from NN after postnatal HFD


title: Day3 3Gy rep14


title: Day3 6Gy rep3


title: liver_NN_HFD_9

source_name: liver tissue from NN after postnatal HFD


title: liver_UN_HFD_11


title: Day3 3Gy rep12


title: Day3 3Gy rep16


title: liver_UN_RCD_6

description: gene expression data at 9 weeks; liver tissue from UN before HFD

source_name: liver tissue from UN before HFD

value: before HFD

value: 9 weeks


title: liver_NN-Veh_HFD_15


title: liver_NN_HFD_7


title: Day3 3Gy rep13

value: whole blood


title: liver_UN_RCD_5

value: undernourished


title: Day3 3Gy rep10


title: Day3 6Gy rep8


title: Day3 3Gy rep11


title: liver_NN_HFD_8


title: liver_NN_RCD_2

description: gene expression data at 9 weeks; liver tissue from NN before HFD

source_name: liver tissue from NN before HFD


title: liver_NN-TU_HFD_22

value: postnatal HFD with TUDCA


title: liver_UN_RCD_4

value: Male


title: Decliner #2

city: Sao Paulo

first: Maria Beatriz

last: Monteiro

address: Av Dr Arnaldo 455

country: Brazil

institute: University of Sao Paulo Medical School

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using STAR v2.5.2_b with parameters --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsType EndToEnd --sjdbScore 1
counts were generated by featureCounts v1.5.1 with parameters -p -t exon -g gene_id -B -T8 -M -O --fraction
normalized log2-transformed count table was generated by the voom function from the R/Bioconductor limma package
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited matrices including raw counts and log2-normalized counts for all samples

source_name: urine sediment cells

extract_protocol:
Fresh urine specimens were collected in sterile RNAse-free flasks and kept in ice. Total RNA was isolated using Trizol reagent and RNeasy Minikit. RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold® from 100 ng of purified total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols using Illumina TruSeq RNA Sample Prep Kit

value: kidney/urinary tissue

tag: cell type

value: urine sediment cells

value: adult

tag: phenotype

value: renal function:decliner

tag: diagnosis

value: type 1 diabetes


title: Non-Decliner #2

value: renal function:non-decliner


title: Non-Decliner #1


title: Decliner #1


title: Decliner #4


title: Day3 3Gy rep3


title: Non-Decliner #3


title: liver_NN_RCD_1

value: normal nutrition

value: Liver


title: Day3 3Gy rep2

value: Day3 3Gy


title: Control #2

value: control

value: healthy control


title: Day3 1.5Gy rep5

value: male

value: 8-10 weeks

value: Day3 1.5Gy


title: Day3 1.5Gy rep6

value: whole blood


title: Day3 1.5Gy rep1


title: Day3 1.5Gy rep4


title: Day3 1.5Gy rep3


title: Day3 3Gy rep1


title: Day3 1.5Gy rep2


title: Control #1


title: Decliner #3


title: Day3 6Gy rep7

value: Day3 6Gy


title: RNAseq_hESC_3_untransfected

city: Boston

first: Martha

middle: L.

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

description: genomic RNA

data_processing:
For MPRA samples, we used cutadapt to remove adapters from the raw reads and trim bases with a Phred score < 20. We then counted barcodes if they exactly matched an 11-bp barcode in the design index as well as the constant upstream 6 bp. All scripts used for subsequent data analysis of processed files can be found at https://github.com/kmattioli/2019__cis_trans_MPRA
For RNA-seq samples, we used Hisat2 to align reads hg19 or mm10. We used FeatureCounts to assign reads to genes in GENCODE v25 (lifted to hg19) and GENCODE vM13 (mm10).
Supplementary_files_format_and_content: Barcode counts and gene featureCounts.  The file index.txt.gz contains the chromosomal information for each barcode. This file is also available at: https://github.com/kmattioli/2019__cis_trans_MPRA/blob/master/data/01__design/02__index/index.txt.gz

source_name: HUES64 cell line

growth_protocol: HUES64 cells were cultured in feeder-free mTeSR1 media and passaged every 5-7 days. mESC cells were cultured in feeder-free 2i media and passaged every 3-5 days.

extract_protocol:
RNA from transiently transfected cells was precipitated by phenol-chloroform extraction according to standard protocols. DNase treatment (Worthington) was followed by cDNA synthesis with SuperScript III First-Strand Synthesis System (Invitrogen).
cDNA was subject to library amplification and libraries were cleaned up with AMPure beads (0.6x, 1.6x, 1.0x).

treatment_protocol: Three different passaged of HUES64 cells were transiently transfected in triplicate (2.5 million cells each with 25 µg plasmid using 60 µL LipofectStem). Three different passages of mESC cells were transiently transfected (10 million cells each with 40 µg plasmid using 100 µL Lipofectamine 2000).

value: HUES64 cell line

tag: experiment

value: RNA-seq


title: RNAseq_hESC_3_transfected_Rep3

description: genomic RNA


title: Non-Decliner #4

value: kidney/urinary tissue

value: urine sediment cells


title: Day3 Control rep9

source_name: whole blood_Day3 Control

value: Day3 Control


title: Day3 Control rep7


title: Day3 Control rep6


title: Day3 Control rep10


title: RNAseq_hESC_3_transfected_Rep2

description: genomic RNA


title: Day3 Control rep8


title: RNAseq_hESC_3_transfected_Rep1

description: genomic RNA


title: RNAseq_hESC_2_transfected_Rep2

description: genomic RNA


title: RNAseq_hESC_2_transfected_Rep1

description: genomic RNA


title: RNAseq_hESC_1_untransfected

description: genomic RNA


title: RNAseq_hESC_1_transfected_Rep2

description: genomic RNA


title: RNAseq_hESC_2_untransfected

description: genomic RNA


title: RNAseq_hESC_2_transfected_Rep3

description: genomic RNA


title: liver_UN_HFD_12

value: undernourished

value: postnatal HFD

value: Male

value: 17 weeks


title: Day3 Control rep2


title: Day3 10Gy rep14

value: Day3 10Gy


title: Day3 Control rep4


title: Day3 10Gy rep13


title: RNAseq_hESC_1_transfected_Rep3

description: genomic RNA


title: Day3 10Gy rep12


title: MPRA__HUES64__rep3__tfxn1

description: GFP RNA

data_processing:
Library strategy: MPRA
For MPRA samples, we used cutadapt to remove adapters from the raw reads and trim bases with a Phred score < 20. We then counted barcodes if they exactly matched an 11-bp barcode in the design index as well as the constant upstream 6 bp. All scripts used for subsequent data analysis of processed files can be found at https://github.com/kmattioli/2019__cis_trans_MPRA
For RNA-seq samples, we used Hisat2 to align reads hg19 or mm10. We used FeatureCounts to assign reads to genes in GENCODE v25 (lifted to hg19) and GENCODE vM13 (mm10).
Supplementary_files_format_and_content: Barcode counts and gene featureCounts.  The file index.txt.gz contains the chromosomal information for each barcode. This file is also available at: https://github.com/kmattioli/2019__cis_trans_MPRA/blob/master/data/01__design/02__index/index.txt.gz

value: MPRA


title: MPRA__HUES64__rep3__tfxn2

description: GFP RNA


title: MPRA__HUES64__rep2__tfxn3

description: GFP RNA


title: Day3 Control rep5


title: MPRA__HUES64__rep3__tfxn3

description: GFP RNA


title: Day3 10Gy rep8


title: Day3 Control rep1


title: RNAseq_hESC_1_transfected_Rep1

description: genomic RNA


title: Day3 10Gy rep10


title: MPRA__HUES64__rep2__tfxn2

description: GFP RNA


title: Day3 Control rep3


title: Day3 10Gy rep5


title: MPRA__HUES64__rep2__tfxn1

description: GFP RNA


title: MPRA__HUES64__rep1__tfxn2

description: GFP RNA


title: MPRA__HUES64__rep1__tfxn3

description: GFP RNA


title: Day3 10Gy rep6


title: Day3 10Gy rep7


title: MPRA__HUES64__rep1__tfxn1

description: GFP RNA


title: Day2 6Gy rep14

source_name: whole blood_Day2 6Gy

value: Day2 6Gy


title: Day2 10Gy rep14

source_name: whole blood_Day2 10Gy

value: male

value: Day2 10Gy


title: Day2 6Gy rep15

value: 8-10 weeks


title: Day3 10Gy rep9

value: whole blood


title: liver_NN_RCD_3

value: normal nutrition

value: before HFD

value: Liver

value: 9 weeks


title: Day2 6Gy rep13


title: VF rep5 [S26_VFs]

city: Madison

first: Ziyue

last: Wang

state: WI

address: 425 Henry Mall

institute: UW Madison

data_processing:
bcl2fastq-1.8.4 software was used for basecalling
Sequencing reads were mapped to the hg19 genome using the short-read aligner Bowtie v1.0.0 (Langmead et al., 2009)
The transcript expected countx were estimated using RSEM v1.2.7 (Li et al., 2011) with parameters -p 5 and then normalized by the size of the library using EBSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include expected count values for each sample; a csv file for normalized count data for all samples

source_name: vocal fold_fibroblast cells

growth_protocol: All tissue samples were procured from donors within 24 h of death and processed within 1 h of sample harvesting. Culture methodology involved mincing tissue samples into small pieces (1 X 1 mm) with a sterile scalpel blade and placing these into cell culture dishes precoated with minimum essential medium Eagle with Earle’s balanced salt solutions supplemented with 1X nonessential amino acids, 1X antibiotic-antimycotic, and 10% fetal bovine serum. Tissue samples were not disturbed for 5 days to ensure adherence to the Petri dish. The dishes were kept at 37°C in a cell culture incubator with 5% CO2-95% air.

extract_protocol:
To obtain total RNA, cultured fibroblasts were trypsinized and harvested at a density no less than 1 X 106. Cells were then neutralized with fresh media and centrifuged at 1000 rpm for 10 min to retrieve the cell pellet. Total RNA was purified from cell pellet samples using the RNeasy Mini Kit (Cat No. 74106) (QIAGEN) according to the manufacturer’s protocol. RNase-free DNase (QIAGEN) was treated on the column for 15 min to remove the minimum genomic DNA contamination. Quantification of all total RNA samples, initially, were performed using a NanoDrop 1000 spectrophotometer (Thermo Scientific), and integrity of samples were confirmed with the following three criteria for inclusion: (1) a concentration > 40 ng/ml, (2) an A260/A280 rating of 1.8 and 2.1, and (3) an A260/A230 ratio > 1.8.
Total RNA submitted to the University of Wisconsin-Madison Biotechnology Center was verified for purity and integrity via the NanoDrop One Spectrophotometer and Agilent 2100 BioAnalyzer, respectively. Samples that met the Illumina sample input guidelines were prepared according the TruSeq® Stranded mRNA Sample Preparation Guide (Rev. E) using the Illumina® TruSeq® Stranded mRNA Sample Preparation kits (Illumina Inc., San Diego, California, USA). For each library preparation, mRNA was purified from 1μg total RNA using poly-T oligo-attached magnetic beads. Subsequently, each poly-A enriched sample was fragmented using divalent cations under increased temperature. The fragmented RNA was synthesized into double-stranded cDNA using SuperScript II Reverse Transcriptase (Invitrogen, Carlsbad, California, USA) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA Polymerase I and RNAse H for removal of mRNA. Double-stranded cDNA was purified by paramagnetic beads (Agencourt AMPure XP beads, Beckman Coulter). The cDNA products were incubated with Klenow DNA Polymerase to add an ‘A’ base (Adenine) to the 3′ end of the blunt DNA fragments. DNA fragments were ligated to Illumina adapters, which have a single ‘T’ base (Thymine) overhang at their 3′ end. Adapter-ligated DNA products were purified by paramagnetic beads, successively amplified in a Linker Mediated PCR reaction (LM-PCR) for nine cycles using Phusion™ DNA Polymerase and Illumina’s PE genomic DNA primer set and then purified by paramagnetic beads. Quantity and quality of completed libraries were evaluated using a Qubit® dsDNA HS Assay Kit (Invitrogen, Carlsbad, California, USA), and an Agilent HS DNA or DNA1000 chip (Agilent Technologies, Inc., Santa Clara, CA, USA), respectively. Libraries were standardized to 2 nM. Cluster generation was executed using standard Cluster Kits (v4) and the Illumina cBot. Single end, 100 bp sequencing was completed using standard SBS chemistry (v4) on an Illumina HiSeq2500 sequencer. Images were analyzed using the standard Illumina Pipeline, version 1.8.2.

treatment_protocol: To allow for optimized cell proliferation and migration from original explants, medium was renewed every 2 to 3 days. Upon reaching subconfluence (e.g. 80–90% confluent), cells were trypsinized and passed to T75 flasks for downstream cell seeding. Passaging ratios between 1:2 and 1:4 were utilized for seeding of cells into 10 cm culture dishes at defined cell densities based upon manual counting of trypsinized cell suspensions using a hemocytometer and subsequent cell concentration calculations. For this experiment, fibroblast cells from passage 3 and 4 were utilized for RNA harvest.

tag: donor age

tag: donor sex

value: F

tag: tissue source

value: vocal fold

value: primary fibroblast populations

tag: passage


title: Gingiva rep5 [S26_Gingiva]

source_name: upper gingiva_fibroblast cells

value: upper gingiva


title: Lung rep3 [S25_Lung]

source_name: lung_fibroblast cells

value: M

value: lung


title: Day2 6Gy rep11

tag: strain


title: Day2 10Gy rep13

tag: treatment


title: VF rep4 [S16_VFs]


title: Trachea rep5 [S16_Trachea]

source_name: trachea_fibroblast cells

value: trachea


title: Scalp rep4 [S16_Scalp]

source_name: scalp dermis _fibroblast cells

value: scalp dermis


title: Abs rep4 [S16_Abs]

source_name: abdomen dermis_fibroblast cells

value: abdomen dermis


title: Lung rep5 [S31_Lung]


title: Palate rep4 [S29_Palate]

source_name: soft palate _fibroblast cells

value: soft palate


title: VF rep3 [S15_VFs]


title: Scalp rep5 [S17_Scalp]


title: Lung rep4 [S30_Lung]


title: Day2 6Gy rep8

tag: Sex

value: male

value: Day2 6Gy


title: Day2 6Gy rep9

value: 8-10 weeks

value: whole blood


title: Trachea rep4 [S15_Trachea]


title: Day2 6Gy rep7


title: Day2 3Gy rep12

source_name: whole blood_Day2 3Gy

value: Day2 3Gy


title: Day2 3Gy rep11


title: Day2 3Gy rep13


title: Day2 6Gy rep6


title: Abs rep5 [S17_Abs]


title: Day2 3Gy rep8


title: Gingiva rep4 [S15_Gingiva]


title: Day2 6Gy rep10


title: Trachea rep3 [S13_Trachea]


title: Lung rep2 [S15_Lung]


title: Trachea rep2 [S09_Trachea]


title: Day2 3Gy rep6


title: Abs rep3 [S12_Abs]


title: Day2 3Gy rep9


title: Day2 6Gy rep1


title: Scalp rep2 [S09_Scalp]


title: Palate rep3 [S09_Palate]


title: Day2 3Gy rep2


title: Gingiva rep3 [S09_Gingiva]


title: Abs rep2 [S09_Abs]


title: Day2 3Gy rep7


title: VF rep2 [S08_VFs]


title: Scalp rep3 [S12_Scalp]


title: Day2 3Gy rep1


title: Day2 1.5Gy rep9

source_name: whole blood_Day2 1.5Gy

value: Day2 1.5Gy


title: Day2 1.5Gy rep7


title: Day2 1.5Gy rep1


title: Day2 Control rep9

source_name: whole blood_Day2 Control

value: Day2 Control


title: Day2 1.5Gy rep10


title: Palate rep2 [S08_Palate]


title: VF rep1 [S06_VFs]


title: Day2 3Gy rep5


title: Trachea rep1 [S06_Scalp]


title: Scalp rep1 [S06_Palate]


title: Day2 Control rep4


title: Day2 Control rep8


title: Gingiva rep1 [S06_Gingiva]


title: Day2 Control rep7


title: Day2 Control rep6


title: Day2 Control rep10


title: Abs rep1 [S03_Abs]


title: Gingiva rep2 [S08_Gingiva]


title: Day2 Control rep3


title: Day2 Control rep2


title: Palate rep1 [S06_Trachea]


title: HUES_1_WT_differentiation_replicate_3

city: Cambridge

first: Lee

middle: L

last: Rubin

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
Each library was sequenced to a depth of ∼60 million fragments using 50 bp paired-end reads.
RNA-seq reads were mapped using TopHat version 2.0.9 against the human genome build GRCh38. The primary assembly was downloaded from primary assembly from ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/dna/. FASTQ files were aligned to the primary assembly ENSEMBL GRCh38 index built ftp://ftp.ensembl.org/pub/release-85/fasta/homo_sapiens/dna/ using Tophat. F
or annotations, we used a GTF transcriptome build GRCh38 here: ftp://ftp.ensembl.org/pub/release-85/gtf/homo_sapiens.
Genome_build: hg19

source_name: TH fluorescence reporter sorted DNs d35

extract_protocol:
Methods: RNA extraction for mRNA sequencing was performed post flow sorting of at least 200,000 TH+ cells using Qiagen micro RNA extraction with on-column DNase digest. RNA amount and integrity were approximated using the bioanalyzer 2100 RNA Nano kit.
Illumina mRNA-seq libraries were prepared using the TruSeq RNA kit using 200 ng of total RNA per sample.
Library sequencing was carried out on a HiSeq2500 in rapid mode, 1 lane/pool. Each pool contained 6 samples, 3 differentiation replicates per isogenic cell line. The concentration of both pools was approximately 2.6 ng/µl and

value: dopaminergic neuron

tag: genotype

value: WT


title: Day2 Control rep1


title: HUES_1_ATP13A2-/--/-_differentiation_replicate_3


title: HUES_1_PARKIN-/-_differentiation_replicate_3

value: PARKIN-/-


title: HUES_1_DJ-1-/-_differentiation_replicate_3


title: Day2 1.5Gy rep6


title: HUES_1_DJ-1-/-_differentiation_replicate_2


title: HUES_1_ATP13A2-/--/-_differentiation_replicate_2


title: Day2 Control rep5


title: HUES_1_PARKIN-/-_differentiation_replicate_2


title: Day2 1.5Gy rep3


title: Day2 1.5Gy rep5


title: HUES_1_WT_differentiation_replicate_2


title: Day2 10Gy rep12

value: Day2 10Gy


title: Day2 10Gy rep11


title: HUES_1_DJ-1-/-_differentiation_replicate_1


title: Day2 10Gy rep7


title: HUES_1_PARKIN-/-_differentiation_replicate_1


title: Day2 10Gy rep4


title: HUES_1_WT_differentiation_replicate_1


title: Day2 10Gy rep5


title: Day2 1.5Gy rep4


title: HeLa.SMG1_poisonExon

city: Seattle

first: James

middle: Douglas

last: Thomas

state: WA

address: 1100 Fairview Ave. N., B3-111

department: Computational Biology

institute: Fred Hutchinson Cancer Research Center

description: RNA-seq of cell treated with the indicated pgRNA vector.

data_processing:
Illumina Casava software was used for base calling.
For RNA-seq, reads were aligned to the human transcriptome using RSEM followed by mapping to the human genome (hg19) using Bowtie and TopHat.
Gene expression estimates (TPM) were computed using RSEM and normalized using the TMM method.
Differentially expressed genes were defined as those passing specified Bayes factor (computed using Wagenmakers’s Bayesian framework) and fold-change threshold.
Genome_build: hg19
Supplementary_files_format_and_content: The final processed data is found in the file "d.expr.txt"

extract_protocol:
For RNA-seq, all samples were collected into TRIzol and stored at -80°C until RNA was isolated. For pgRNA-seq, genomic DNA was extracted and stored at -20°C.
For RNA-seq, polyA-selected libraries were generated using the Illumina TruSeq kit.

tag: cell line

value: HeLa


title: Day2 10Gy rep1


title: 10X1-

city: Los Angeles

first: William

last: Lowry

address: 621 Charles Young

institute: UCLA

data_processing:
Dropseq pipeline standard parameters. (http://mccarrolllab.org/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1.2Jan2016.pdf)
Data mapped to GRCh38 genome using hisat2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text files of read counts for each sample

source_name: hair follicle

growth_protocol: Single cell suspensions were generated from the micrografts as previously described (Ohyama, Vogel JCI 2006). Briefly, the grafts were flushed with PBS and incubated in dispase overnight at 4oC. The following day, the grafts were incubated in the same dispase solution at 37oC for 30 minutes. Hair grafts were gently dissociated with a P1000 pipette then incubated for 10 minutes in trypsin 0.05% solution diluted with PBS. The grafts were again gently dissociated with P1000 pipette and placed back in 37oC for 10 minutes. Trypsin was deactivated with 5% FBS.  Fibrous tissue and debris were filtered out with a 40um strainer. Single cells were visualized and counted with a hemocytometer and washed with PBS. Live cells were preferentially sorted using a FACS Aria III High-speed Cell Sorter and submitted for single cell sequencing.

extract_protocol:
RNA was extracted using the standard drop-seq pipeline as described in Macosko et al (2015).
As per manufacturers instructions for the Illumina Nextera XT DNA library preparation kit

treatment_protocol: not applicable

tag: sample type

value: single cell suspension


title: Day2 10Gy rep2


title: 10X2-


title: HUES_1_ATP13A2-/--/-_differentiation_replicate_1


title: DS3-


title: DS2-


title: HeLa.CPSF4_poisonExon


title: DS1-


title: Day 1 10Gy rep10

source_name: whole blood_Day 1 10Gy

value: Day 1 10Gy


title: RNAseq_CB3_Day4_UM171_SR1

city: Toronto

first: Stephanie

middle: Zhi-Juan

last: Xie

state: ON

address: 101 College St. TMDT 8-401

country: Canada

institute: University Health Network

description:
Cord blood 3
RNAseq at day 4

data_processing:
Reads were trimmed to remove the adapters and were then aligned to hg19 using TopHat (v2.1.1) and gene counts were generated using HTSeq (v 0.6.1)
Genome_build: hg19
Supplementary_files_format_and_content: Read counts per gene per sample (tsv)

source_name: lineage depleted human cord blood cells

growth_protocol: Three pools of lin- CB at the 16 LTRC dose (62,500 cells/well, 24 well plate) were cultured with StemPro (Stem Cell Technologies) supplemented with StemPro nutrients (Stem Cell Technologies), L-glutamine (GIBCO), Pen/Strep (GIBCO), human LDL (Stem Cell Technologies, 50 ng/mL) and the following cytokines (all from Miltenyi): SCF (100 ng/mL), Flt3L (20 ng/mL), TPO (100 ng/mL), EPO (3 units/mL), IL-6 (50 ng/mL), IL-3 (10 ng/mL), GM-CSF (20 ng/mL).

extract_protocol:
RNA was isolated with the RNeasy microRNA plus kit (Qiagen).
Nextera libraries were generated without amplification from 500 ng RNA and subjected to 125 bp, paired-end RNA-sequencing on the Illumina HiSeq 2500 with an average of ~57 million reads/sample.

treatment_protocol: DMSO, 2μM 4HPR, 35nM UM171 + 500 nM SR1 (U+S) or combination of 4HPR+UM171+SR1 (3-Factor) were added to cells and media at day 0 for collection of cells at day 2 for RNA isolation or added at both day 0 and day 2 for collection of cells at day 4 for RNA isolation.

tag: pool

value: Cord blood

tag: culture time

value: 4 days

tag: small molecule treatment


title: Day 1 10Gy rep 6

tag: age

tag: tissue


title: Day 1 10Gy rep 5


title: Day 1 10Gy rep 7


title: Day 1 10Gy rep 3


title: Day 1 10Gy rep 4


title: Day 1 10Gy rep 2


title: Day 1 10Gy rep 1


title: Lung rep1 [S04_Lung]

value: F

value: lung

tag: cell type

value: primary fibroblast populations


title: Day 1 10Gy rep 9

value: male

value: 8-10 weeks


title: Day2 1.5Gy rep8

value: whole blood


title: RNAseq_CB3_Day2_3Combo

description:
Cord blood 3
RNAseq at day 2

value: 2 days


title: RNAseq_CB3_Day2_UM171_SR1

description:
Cord blood 3
RNAseq at day 2


title: RNAseq_CB3_Day2_DMSO

description:
Cord blood 3
RNAseq at day 2

value: DMSO


title: RNAseq_CB3_Day2_4HPR

description:
Cord blood 3
RNAseq at day 2


title: RNAseq_CB3_Day4_3Combo

description:
Cord blood 3
RNAseq at day 4


title: Day1 6Gy rep9

source_name: whole blood_Day1 6Gy

value: Day1 6Gy


title: Day1 6Gy rep10


title: RNAseq_CB3_Day0_Untreated

description:
Cord blood 3
RNAseq at day 0

value: 0 days

value: Untreated


title: Day1 3Gy rep10

source_name: whole blood_Day1 3Gy

value: Day1 3Gy


title: RNAseq_CB3_Day4_4HPR

description:
Cord blood 3
RNAseq at day 4


title: RNAseq_CB2_Day4_3Combo

description:
Cord blood 2
RNAseq at day 4


title: Day1 1.5Gy rep10

source_name: whole blood_Day1 1.5Gy

value: Day1 1.5Gy


title: Day1 1.5Gy rep 9


title: RNAseq_CB2_Day4_UM171_SR1

description:
Cord blood 2
RNAseq at day 4


title: RNAseq_CB2_Day4_4HPR

description:
Cord blood 2
RNAseq at day 4


title: RNAseq_CB2_Day4_DMSO

description:
Cord blood 2
RNAseq at day 4


title: RNAseq_CB2_Day2_3Combo

description:
Cord blood 2
RNAseq at day 2


title: Day1 6Gy rep8


title: Day 1 Control rep 9

source_name: whole blood_Day 1 Control

value: Day 1 Control


title: RNAseq_CB3_Day4_DMSO

description:
Cord blood 3
RNAseq at day 4


title: Day1 6Gy rep7


title: RNAseq_CB2_Day2_4HPR

description:
Cord blood 2
RNAseq at day 2


title: RNAseq_CB2_Day2_UM171_SR1

description:
Cord blood 2
RNAseq at day 2


title: RNAseq_CB2_Day2_DMSO

description:
Cord blood 2
RNAseq at day 2


title: Day1 3Gy rep9


title: Day 1 Control rep10


title: RNAseq_CB1_Day4_3Combo

description:
Cord blood 1
RNAseq at day 4


title: RNAseq_CB1_Day4_4HPR

description:
Cord blood 1
RNAseq at day 4


title: Day1 6Gy rep6


title: RNAseq_CB1_Day4_UM171_SR1

description:
Cord blood 1
RNAseq at day 4


title: RNAseq_CB1_Day4_DMSO

description:
Cord blood 1
RNAseq at day 4


title: RNAseq_CB1_Day2_3Combo

description:
Cord blood 1
RNAseq at day 2


title: RNAseq_CB1_Day2_UM171_SR1

description:
Cord blood 1
RNAseq at day 2


title: Day1 3Gy rep6


title: Day1 3Gy rep8


title: Day1 3Gy rep5


title: Day1 1.5Gy rep 7


title: RNAseq_CB1_Day2_4HPR

description:
Cord blood 1
RNAseq at day 2


title: Day1 3Gy rep7


title: Day1 1.5Gy rep 6


title: Day1 6Gy rep5


title: ATACseq_P7_Combo_CB4

description: Cord blood 4

data_processing:
Each sample was aligned against hg19 using BWA with default parameters. All reads mapping to hg19 blacklist regions, mitochondrial genome, chrY or non-autosomal regions were removed. All reads with a quality score < 30 were removed.
MACS2 was used to identify significantly enriched regions of chromatin in each sample using default parameters plus the -llocal and -SPMR parameters.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak File

growth_protocol: Lin- CB at the 16 LTRC dose (62,500 cells/well, 24 well plate) were cultured with StemPro (Stem Cell Technologies) supplemented with StemPro nutrients (Stem Cell Technologies), L-glutamine (GIBCO), Pen/Strep (GIBCO), human LDL (Stem Cell Technologies, 50 ng/mL) and the following cytokines (all from Miltenyi): SCF (100 ng/mL), Flt3L (20 ng/mL), TPO (100 ng/mL), EPO (3 units/mL), IL-6 (50 ng/mL), IL-3 (10 ng/mL), GM-CSF (20 ng/mL) for 8 days.

extract_protocol:
Library preparation for ATAC-Sec was performed on 30,000 cells with Nextera DNA Sample Preparation kit (FC-121-1030, Iillumina), according to previously reported protocol (Buenrostro et al. 2013).
Libraries for ATAC were sequenced with HiSeq 2500 System (Illumina) to generate single-end 50-bp reads.

treatment_protocol: Cells were untreated, or DMSO, 2μM 4HPR, 35nM UM171 + 500 nM SR1 (U+S) or combination of 4HPR+UM171+SR1 (3-Factor) were added to cells and media at day 0. We mimicked fed-batch growth conditions where drug was added with fresh media every second day  for 8 days to reduce auto-inhibitory signalling and ensure nutrients and drugs are not limiting during the culture period (Csaszar et al., 2012): fresh media plus drugs are added on day 2 (0.5mls), day 4 (1ml), and feeding and transferring to a 6 well plate on day 6 (2 mls). Following ex vivo culture for 8 days, 4 pools of expanded lin-CB cells in the presence of indicated compounds were collected and subjected to CD34 enrichment with the CD34 Microbead kit (Miltenyi) on LS columns (Miltenyi). CD34+ enriched cells were then stained with CD45RA-FITC, CD90-PE, CD34 APC-cy7, and propidium iodide (PI) and 30,000 cLT (CD34+CD90+CD45RA-PI-) and cST (CD34+CD90-CD45RA-PI-) were sorted on the FACSAria Fusion (BD).

value: cord blood

tag: immunophenotypic cell population

value: cST


title: RNAseq_CB1_Day2_DMSO

description:
Cord blood 1
RNAseq at day 2

value: Cord blood


title: ATACseq_P6_Combo_CB4

description: Cord blood 4

value: cLT


title: ATACseq_P7_US_CB4

description: Cord blood 4


title: Day1 1.5Gy rep 5


title: ATACseq_P6_US_CB4

description: Cord blood 4


title: ATACseq_P7_4HPR_CB4

description: Cord blood 4


title: Day 1 Control rep 8


title: Day 1 Control rep 7


title: Day 1 Control rep 6


title: ATACseq_P6_4HPR_CB4

description: Cord blood 4


title: Day1 1.5Gy rep 8


title: Day 1 Control rep 5


title: ATACseq_P7_DMSO_CB4

description: Cord blood 4


title: Day 1_6Gy rep1

source_name: whole blood_Day 1_6Gy

value: Day 1_6Gy


title: Day1_6Gy rep3

source_name: whole blood_Day1_6Gy


title: Day 1_6Gy rep2


title: ATACseq_P7_None_CB4

description: Cord blood 4

value: untreated


title: ATACseq_P6_DMSO_CB4

description: Cord blood 4


title: Day1_6Gy rep4

value: male


title: ATACseq_P7_Combo_CB3

description: Cord blood 4


title: ATACseq_P6_None_CB4

description: Cord blood 4


title: Day1_3 Gy rep3

source_name: whole blood_Day1_3 Gy

value: 8-10 weeks

value: Day1_3 Gy


title: Day 1_3 Gy rep1

source_name: whole blood_Day 1_3 Gy

value: Day 1_3 Gy

value: whole blood


title: Day2 1.5Gy rep2

value: Day2 1.5Gy


title: Day1_3 Gy rep4


title: ATACseq_P6_US_CB3

description: Cord blood 3


title: ATACseq_P7_US_CB3

description: Cord blood 3


title: Day 1_3 Gy rep2


title: ATACseq_P6_None_CB3

description: Cord blood 3


title: Day 1_1.5 Gy rep 4

source_name: whole blood_Day 1_1.5 Gy

value: Day 1_1.5 Gy


title: ATACseq_P7_US_CB2

description: Cord blood 2


title: ATACseq_P7_Combo_CB2

description: Cord blood 3


title: ATACseq_P6_Combo_CB2

description: Cord blood 3


title: ATACseq_P6_US_CB2

description: Cord blood 2


title: Day 1 10Gy rep 8

value: Day 1 10Gy


title: ATACseq_P7_4HPR_CB2

description: Cord blood 2